[English] 日本語
Yorodumi
- PDB-3mj9: Crystal structure of JAML in complex with the stimulatory antibod... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3mj9
TitleCrystal structure of JAML in complex with the stimulatory antibody HL4E10
Components
  • Junctional adhesion molecule-like
  • STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN
  • STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN TANDEM DOMAIN / RECEPTOR-ANTIBODY COMPLEX / CELL ADHESION / CELL JUNCTION / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / MEMBRANE / COSTIMULATION / HAMSTER IgG / TRANSMEMBRANE
Function / homology
Function and homology information


monocyte extravasation / Cell surface interactions at the vascular wall / gamma-delta T cell activation / neutrophil extravasation / positive regulation of epithelial cell proliferation involved in wound healing / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis ...monocyte extravasation / Cell surface interactions at the vascular wall / gamma-delta T cell activation / neutrophil extravasation / positive regulation of epithelial cell proliferation involved in wound healing / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / integrin binding / protein homodimerization activity / nucleoplasm / plasma membrane
Similarity search - Function
Myelin P0 protein-related / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain ...Myelin P0 protein-related / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Junctional adhesion molecule-like
Similarity search - Component
Biological speciesMus musculus (house mouse)
CRICETULUS MIGRATORIUS (Armenian hamster)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsVerdino, P. / Wilson, I.A.
CitationJournal: Structure / Year: 2011
Title: Molecular insights into gamma delta T cell costimulation by an anti-JAML antibody.
Authors: Verdino, P. / Witherden, D.A. / Ferguson, M.S. / Corper, A.L. / Schiefner, A. / Havran, W.L. / Wilson, I.A.
History
DepositionApr 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Junctional adhesion molecule-like
L: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN
H: STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,5856
Polymers77,0853
Non-polymers1,4993
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7600 Å2
ΔGint-3 kcal/mol
Surface area30250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.020, 125.020, 107.839
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

-
Components

#1: Protein Junctional adhesion molecule-like / / Dendritic cell-specific protein CREA7 / mCrea7


Mass: 30647.387 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (UNP RESIDUES 21-280) / Mutation: K124R, R211Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Amica1, Gm638, Jaml / Plasmid: PMT/BIP/V5-HIS A / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q80UL9
#2: Antibody STIMULATORY HAMSTER ANTIBODY HL4E10 FAB LIGHT CHAIN


Mass: 22784.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC
Source: (natural) CRICETULUS MIGRATORIUS (Armenian hamster) / Strain: HYBRIDOMA
#3: Antibody STIMULATORY HAMSTER ANTIBODY HL4E10 FAB HEAVY CHAIN


Mass: 23653.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC
Source: (natural) CRICETULUS MIGRATORIUS (Armenian hamster) / Strain: HYBRIDOMA
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 1.2-1.4 M NA-MALONATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2006
Details: SI(111) DOUBLE CRYSTAL MONOCHROMATOR. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY
RadiationMonochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.95→30 Å / Num. obs: 18365 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 6.8
Reflection shellResolution: 2.95→3.06 Å / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.617 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHASERphasing
REFMAC5.4.0069refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.875 / SU B: 42.292 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.287 927 5.1 %RANDOM
Rwork0.222 ---
obs0.225 17200 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 77.244 Å2
Baniso -1Baniso -2Baniso -3
1--1.23 Å20 Å20 Å2
2---1.23 Å20 Å2
3---2.46 Å2
Refinement stepCycle: LAST / Resolution: 2.95→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4995 0 99 0 5094
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0225217
X-RAY DIFFRACTIONr_bond_other_d0.0010.023452
X-RAY DIFFRACTIONr_angle_refined_deg1.0611.9687109
X-RAY DIFFRACTIONr_angle_other_deg1.3033.0038421
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1385644
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.30824.408211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.48215844
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.6681524
X-RAY DIFFRACTIONr_chiral_restr0.0660.2829
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0215696
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02994
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1310.2145
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0250.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1320.238
X-RAY DIFFRACTIONr_symmetry_vdw_other0.150.2105
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.120.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.60633219
X-RAY DIFFRACTIONr_mcbond_other0.07131310
X-RAY DIFFRACTIONr_mcangle_it1.21755231
X-RAY DIFFRACTIONr_scbond_it1.98271998
X-RAY DIFFRACTIONr_scangle_it3.516111878
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.95→3.03 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.48 72 -
Rwork0.295 1246 -
obs--98.95 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.5050.59420.98682.4241.179210.2021-0.05290.04180.14730.0031-0.00790.1462-0.1466-0.23870.0608-0.36650.0280.107-0.17010.1443-0.1724-12.5149-56.1071-16.8211
22.65070.5765-0.09013.31781.68329.87660.0128-0.1190.60090.59170.21060.2432-0.6346-0.5688-0.2234-0.04360.12460.307-0.28580.1071-0.0688-5.6331-33.74130.5488
39.8096-0.6537-0.54055.71291.64984.15530.31460.0910.22450.955-0.1948-0.4588-0.23090.2154-0.1198-0.1259-0.05570.0436-0.44290.1665-0.297917.223-32.6237-15.4424
44.1748-1.10670.98963.19220.27810.7383-0.28150.33480.05570.07470.2846-0.77960.04470.401-0.0031-0.0998-0.2063-0.04560.0049-0.23180.246337.3773-44.5855-46.8504
55.21080.4218-2.22132.7162-2.14999.933-0.18440.90780.36160.0830.40350.4913-0.2921-0.4859-0.2191-0.38270.09680.0882-0.07040.1896-0.13193.8831-28.0776-32.563
64.1028-1.89010.561210.0859-0.27814.08640.06920.1445-0.548-0.16190.2135-0.21910.3971-0.2934-0.2827-0.126-0.2723-0.07080.3302-0.0431-0.207421.3906-47.0282-48.0561
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A8 - 121
2X-RAY DIFFRACTION1A301 - 506
3X-RAY DIFFRACTION2A122 - 236
4X-RAY DIFFRACTION3L2 - 108
5X-RAY DIFFRACTION4L109 - 212
6X-RAY DIFFRACTION5H1 - 113
7X-RAY DIFFRACTION6H114 - 228

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more